From owner-chemistry@ccl.net Tue Jun 25 07:12:01 2013 From: "Scott Mckechnie jsm78#%#cam.ac.uk" To: CCL Subject: CCL: Spikes in PM6 optimization energies Message-Id: <-48848-130625071034-4280-ugE2mZtG7pjvNxT0tVQheQ..server.ccl.net> X-Original-From: "Scott Mckechnie" Date: Tue, 25 Jun 2013 07:10:33 -0400 Sent to CCL by: "Scott Mckechnie" [jsm78-*-cam.ac.uk] Dear all, I ran a PM6 optimization of an organic molecule and found spikes in the completed SCF cycle energies. For example: SCF Done: E(RPM6) = -0.739823088031E-01 A.U. after 19 cycles SCF Done: E(RPM6) = -0.559900784544E-01 A.U. after 25 cycles SCF Done: E(RPM6) = -0.742045066741E-01 A.U. after 25 cycles - Is this simply a result of an optimization step that goes uphill on the PES? - If an increase in the energy is found will it be discarded and the optimization search will start at the previous point? - Is this type of behaviour also commonly seen in a DFT optimization? Any good references for discussions on this would be greatly appreciated. Best wishes, Scott From owner-chemistry@ccl.net Tue Jun 25 08:41:00 2013 From: "bonoit dahmani bonoit_10- -yahoo.fr" To: CCL Subject: CCL: PhD dissertation defense Message-Id: <-48849-130625035947-18246-j6PmGBbp8XVVIT09Z0ATZA-x-server.ccl.net> X-Original-From: bonoit dahmani Content-Type: multipart/alternative; boundary="-1437147565-1096508151-1372147179=:62711" Date: Tue, 25 Jun 2013 08:59:39 +0100 (BST) MIME-Version: 1.0 Sent to CCL by: bonoit dahmani [bonoit_10^yahoo.fr] ---1437147565-1096508151-1372147179=:62711 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear Kamel Mansouri,=0A=0AThank you very much for the invitation. I wish yo= u a good dissertation and have a good discussion with the jury.=0A=0AWith t= he best wishes=0A=0ABonoir=0A=0A=0A=0A=0A________________________________= =0A De=A0: Teri Robinson mihrtaches%%gmail.com =0A= =C0=A0: "Bonoir, Bonoir " =0AEnvoy=E9 le : Merc= redi 19 juin 2013 18h30=0AObjet=A0: CCL: PhD dissertation defense=0A =0A=0A= =0AGood luck to you Kamel Mansouri!=0A=0A=0A=0AOn Wed, Jun 19, 2013 at 5:30= AM, kamel kamel_mansouri*yahoo.fr wrote:=0A=0A= =0A>Sent to CCL by: kamel [kamel_mansouri*o*yahoo.fr]=0A>Dear CCLers,=0A>= =0A>I have the pleasure to invite you to my PhD dissertation defense entitl= ed: "New molecular descriptors for estimating degradation and fate of organ= ic pollutants by QSAR/QSPR models within REACH". Supervised by Prof. Robert= o Todeschini, in the framework of the ECO-ITN project (http://www.eco-itn.e= u/)=0A>The presentation and discussion will take place on the 27 of June at= the University of Milano Bicocca (Milan, Italy), Department of environment= al sciences (U1). Piazza della scienza, 1 Milano 20126 (Italy).=0A>=0A>The = jury:=0A>Prof. Willie PEIJNENBURG, Institute of Environmental Sciences, Uni= versity of Leiden=0A>Prof. Lutgarde BUYDENS, Faculty of Sciences, Radboud U= niversity Nijmegen=0A>Coordinator: Prof. Marco VIGHI, Department of Eniviro= nmental Sciences and Earth, University of Milano-Bicocca=0A>=0A>Abstract:= =0A>Organic pollutants that resist degradation in the environment can accum= ulate in body tissues and cause unavoidable intoxications to organisms in w= ild life as well as humans. The possible effects, usually increasing with t= he cumulative exposure to such chemicals, are not always addressed adequate= ly in risk assessment procedures evaluating long and short-term contact haz= ard. Thus, chemicals accumulation, degradation and environmental fate are o= f prime concern for REACH when defining side effects due to chronic exposur= e.=0A>Characteristics and behavior of organic pollutants have been investig= ated experimentally during the last decades by use of various methods of tr= ace analysis. However, the available data still contains several gaps. In t= his aim, REACH promotes the use of alternative methods to reduce the number= of animal tests and suggests in-silico methods such as Quantitative Struct= ure-Activity Relationships (QSARs) to fill the lack of knowledge.=0A>The go= al of this thesis, in the framework of the ECO-ITN project, was to build QS= AR models with high reliability based on good experimental data for optimal= estimation of environmental endpoints of interest for REACH. New molecular= descriptors and feature selection techniques have been tested paying parti= cular attention to the validation steps and applicability domain definition= .=0A>=0A>Looking forward to seeing you.=0A>=0A>Best regards=0A>=0A>-- =0A>K= amel Mansouri=0A>Milano Chemometrics and QSAR Research Group=0A>Department = of Environmental Sciences=0A>University of Milano-Bicocca - Italy=0A>http:/= /michem.disat.unimib.it/chm/=0A>http://www.eco-itn.eu/=0A>=0A>=0A>=0A>-=3D = This is automatically added to each message by the mailing script =3D-=0A>= =0A>E-mail to subscribers: CHEMISTRY*o*ccl.net or use:=0A>=A0 =A0 =A0http:/= /www.ccl.net/cgi-bin/ccl/send_ccl_message=0A>=0A>E-mail to administrators: = CHEMISTRY-REQUEST*o*ccl.net or use=0A>=A0 =A0 =A0http://www.ccl.net/cgi-bin= /ccl/send_ccl_message=0A>http://www.ccl.net/chemistry/sub_unsub.shtml=0A>= =0A=0A>=0A>Job: http= ://www.ccl.net/jobs Conferences: http://server.ccl.net/chemistry/announceme= nts/conferences/=0A>=0A>Search Messages: http://www.ccl.net/chemistry/searc= hccl/index.shtml=0A>=0A>=A0 =A0 =A0http://www.ccl.net/spammers.txt=0A>=0A>R= TFI: http://www.ccl.net/chemistry/aboutccl/instructions/=0A>=0A>=0A>=0A=0A= =0A-- =0ATeri Lynn Robinson, PhD=0A=0A"That you may retain your self-respec= t, it is better to displease the people by doing what you know is right, th= an to temporarily please them by doing what you know is wrong." -- William = J. H. Boetcker=0A=0A"I prefer to be true to myself, even at the hazard of i= ncurring the ridicule of others, rather than to be false, and to incur my o= wn abhorrence."---Frederick Douglass, an abolitionist ---1437147565-1096508151-1372147179=:62711 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear Kamel Mansouri,<= br>
Thank you very much for the invitation. I wish you a good dissertati= on and have a good discussion with the jury.

With the best wishes
Bonoir


De : Teri Robinson m= ihrtaches%%gmail.com <owner-chemistry(_)ccl.net>
=C0 : "Bonoir, Bonoir " <bono= it_10(_)yahoo.fr>
Envoy=E9 le := Mercredi 19 juin 2013 18h30
Objet : CCL: PhD dissertation defense
 <= /div>

Good luck to you Kamel Mansouri!


On Wed, Jun 19,= 2013 at 5:30 AM, kamel kamel_mansouri*yahoo.fr <owner-chemistry*o*ccl.net> wrote:
=0A=0A

=0ASen= t to CCL by: kamel [kamel_mansouri*o*yahoo.fr]
=0ADear CCLers,
=0A
=0AI h= ave the pleasure to invite you to my PhD dissertation defense entitled: "Ne= w molecular descriptors for estimating degradation and fate of organic poll= utants by QSAR/QSPR models within REACH". Supervised by Prof. Roberto Todes= chini, in the framework of the ECO-ITN project (http://www.eco-itn.eu/)
= =0A=0A=0AThe presentation and discussion will take place on the 27 of June = at the University of Milano Bicocca (Milan, Italy), Department of environme= ntal sciences (U1). Piazza della scienza, 1 Milano 20126 (Italy).
=0A=0AThe jury:
=0AProf. Willie PEIJNENBURG, Institute of Environmental Sc= iences, University of Leiden
=0AProf. Lutgarde BUYDENS, Faculty of Scien= ces, Radboud University Nijmegen
=0ACoordinator: Prof. Marco VIGHI, Depa= rtment of Enivironmental Sciences and Earth, University of Milano-Bicocca=0A
=0AAbstract:
=0AOrganic pollutants that resist degradation in t= he environment can accumulate in body tissues and cause unavoidable intoxic= ations to organisms in wild life as well as humans. The possible effects, u= sually increasing with the cumulative exposure to such chemicals, are not a= lways addressed adequately in risk assessment procedures evaluating long an= d short-term contact hazard. Thus, chemicals accumulation, degradation and = environmental fate are of prime concern for REACH when defining side effect= s due to chronic exposure.
=0A=0A=0ACharacteristics and behavior of orga= nic pollutants have been investigated experimentally during the last decade= s by use of various methods of trace analysis. However, the available data = still contains several gaps. In this aim, REACH promotes the use of alterna= tive methods to reduce the number of animal tests and suggests in-silico me= thods such as Quantitative Structure-Activity Relationships (QSARs) to fill= the lack of knowledge.
=0A=0A=0AThe goal of this thesis, in the framewo= rk of the ECO-ITN project, was to build QSAR models with high reliability b= ased on good experimental data for optimal estimation of environmental endp= oints of interest for REACH. New molecular descriptors and feature selectio= n techniques have been tested paying particular attention to the validation= steps and applicability domain definition.
=0A=0A=0A
=0ALooking forw= ard to seeing you.
=0A
=0ABest regards
=0A
=0A--
=0AKamel M= ansouri
=0AMilano Chemometrics and QSAR Research Group
=0ADepartment = of Environmental Sciences
=0AUniversity of Milano-Bicocca - Italy
=0A= http://michem.disat.unimib.it/chm/
=0Ahttp://www.eco-itn.eu= /
=0A
=0A
=0A
=0A-=3D This is automatically added to each m= essage by the mailing script =3D-
=0A
=0AE-mail to subscribers: CHEMISTRY*o*ccl.net or use:
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=0AE-mail to administrators: CHEMISTRY-REQUEST*o*ccl.net or = use
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=0ABefore posting, check wait time at: http://www.ccl= .net
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=0ARTFI: http://www.ccl.net/chemistry/aboutccl/instructions/
=0A
=0A
=0A


--
Teri Lynn Robinson, PhD

"That you may reta= in your self-respect, it is better to displease the people by doing what yo= u know is right, than to temporarily please them by doing what you know is = wrong." -- William J. H. Boetcker
=0A=0A
"I prefer to be true to myse= lf, even at the hazard of incurring the ridicule of others, rather than to = be false, and to incur my own abhorrence."---Frederick Douglass, an aboliti= onist

=0A


---1437147565-1096508151-1372147179=:62711-- From owner-chemistry@ccl.net Tue Jun 25 09:23:00 2013 From: "John McKelvey jmmckel]![gmail.com" To: CCL Subject: CCL: Spikes in PM6 optimization energies Message-Id: <-48850-130625092112-2630-T6LRId/j8ATa682wA+PshA=-=server.ccl.net> X-Original-From: John McKelvey Content-Type: multipart/alternative; boundary=001a11c29996c87aa404dffa6659 Date: Tue, 25 Jun 2013 09:21:05 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel_+_gmail.com] --001a11c29996c87aa404dffa6659 Content-Type: text/plain; charset=ISO-8859-1 Dcott, Assuming MOPAC2012: At each scf series does the SCF converge rather smoothly? If not try level shifting, SHIFT =15 Graphically I would check the input geometry for unusual distances and angles. Try optimizing the geometry using cartesian coordinates. My $0.02 John McKelvey On Tue, Jun 25, 2013 at 7:10 AM, Scott Mckechnie jsm78#%#cam.ac.uk < owner-chemistry-#-ccl.net> wrote: > > Sent to CCL by: "Scott Mckechnie" [jsm78-*-cam.ac.uk] > Dear all, > > I ran a PM6 optimization of an organic molecule and found spikes in the > completed SCF cycle energies. For example: > > SCF Done: E(RPM6) = -0.739823088031E-01 A.U. after 19 cycles > SCF Done: E(RPM6) = -0.559900784544E-01 A.U. after 25 cycles > SCF Done: E(RPM6) = -0.742045066741E-01 A.U. after 25 cycles > > - Is this simply a result of an optimization step that goes uphill on the > PES? > - If an increase in the energy is found will it be discarded and the > optimization search will start at the previous point? > - Is this type of behaviour also commonly seen in a DFT optimization? > > Any good references for discussions on this would be greatly appreciated. > > Best wishes, > > Scott> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel-#-gmail.com --001a11c29996c87aa404dffa6659 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dcott,

Assuming MOPAC2012:

A= t each scf series does the SCF converge rather smoothly?=A0 If not try leve= l shifting, SHIFT =3D15

=A0Graphically I would check the input geome= try for unusual distances and angles. Try optimizing the geometry using car= tesian coordinates.

My $0.02

John McKelvey=A0
<= br>



On Tue, Jun 25, 2013 at 7:10 AM, Scott Mckechnie jsm78#%#cam.ac.uk <owner-chemistry-#-ccl.net> wrote:

Sent to CCL by: "Scott =A0Mckechnie" [jsm78-*-cam.ac.uk]
Dear all,

I ran a PM6 optimization of an organic molecule and found spikes in the com= pleted SCF cycle energies. For example:

=A0SCF Done: =A0E(RPM6) =3D -0.739823088031E-01 A.U. after =A0 19 cycles =A0SCF Done: =A0E(RPM6) =3D -0.559900784544E-01 A.U. after =A0 25 cycles =A0SCF Done: =A0E(RPM6) =3D -0.742045066741E-01 A.U. after =A0 25 cycles
- Is this simply a result of an optimization step that goes uphill on the P= ES?
- If an increase in the energy is found will it be discarded and the optimi= zation search will start at the previous point?
- Is this type of behaviour also commonly seen in a DFT optimization?

Any good references for discussions on this would be greatly appreciated.
Best wishes,

Scott



-=3D This is automatically added to each message by the mailing script =3D-=
E-mail to subscribers: CHEMISTRY-#-ccl.n= et or use:
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--
John McKelvey
10819 = Middleford Pl
Ft Wayne, IN 46818
260-489-2160
jmmckel-#-gmail.com
--001a11c29996c87aa404dffa6659-- From owner-chemistry@ccl.net Tue Jun 25 12:10:01 2013 From: "Ted Dibble tsdibble-$-esf.edu" To: CCL Subject: CCL: Spikes in PM6 optimization energies Message-Id: <-48851-130625120834-25869-76LhEpaB9XqRzp7YFwl1Gw]~[server.ccl.net> X-Original-From: "Ted Dibble" Date: Tue, 25 Jun 2013 12:08:33 -0400 Sent to CCL by: "Ted Dibble" [tsdibble[*]esf.edu] I see this kind of problem occasionally with DFT optimizations, mostly of transition states. The jump in energy of 0.18 a.u. (~110 kcal/mol) corresponds to a huge amount of energy. I suspect this error arises when the calculation converges on the wrong wavefuntion: that of an excited state. This occurs more readily when bonds are partly broken (transition state searches) than geometry optimizations (unless the initial geometry is poor, as suggested by John McKelvy). If the geometry finally optimizes, it should not be a problem. However, this sort of situation emphasizes the need to check the optimized geometry to make sure you still have the molecule you want. Good Luck! Ted Dibble Theodore S. Dibble Chemistry Department SUNY-Environmental Science and Forestry 1 Forestry Drive Syracuse, NY 13210 (315) 470-6596 (315) 470-6856 (fax) http://www.esf.edu/faculty/dibble/ > "Scott Mckechnie jsm78#%#cam.ac.uk" wrote: > > Sent to CCL by: "Scott Mckechnie" [jsm78-*-cam.ac.uk] > Dear all, > > I ran a PM6 optimization of an organic molecule and found spikes in the completed SCF cycle energies. For example: > > SCF Done: E(RPM6) = -0.739823088031E-01 A.U. after 19 cycles > SCF Done: E(RPM6) = -0.559900784544E-01 A.U. after 25 cycles > SCF Done: E(RPM6) = -0.742045066741E-01 A.U. after 25 cycles > > - Is this simply a result of an optimization step that goes uphill on the PES? > - If an increase in the energy is found will it be discarded and the optimization search will start at the previous point? > - Is this type of behaviour also commonly seen in a DFT optimization? > > Any good references for discussions on this would be greatly appreciated. > > Best wishes, > > Scott > > From owner-chemistry@ccl.net Tue Jun 25 13:45:01 2013 From: "Abrash, Sam sabrash{:}richmond.edu" To: CCL Subject: CCL:G: G09: Proper syntax for CISD Message-Id: <-48852-130625134322-1744-VDZzTojmaUSjWlO/7lle6A**server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640D53Frinzlerrichmond_" Date: Tue, 25 Jun 2013 17:43:14 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash%%richmond.edu] --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640D53Frinzlerrichmond_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi, I submitted a CISD job using the syntax indicated for CIS on page 214 of Ga= ussian's understanding chemistry, but the job crashed because of incorrect = syntax. My .com file was: %chk=3Dpyrimidineisomer3+_1CISD.chk %mem=3D400mw %nproc=3D8 # CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg pyrimidine cation init geom from pyrimidineisomer3+_1.log optimized final C= CSD geometry 1 2 7 -1.013004 -1.023688 0.000000 7 1.257779 -0.459984 0.000000 6 0.229443 -1.329309 0.000000 6 -1.337639 0.290345 0.000000 6 -0.341126 1.285594 0.000000 6 0.986267 0.876632 0.000000 1 -2.405334 0.539673 0.000000 1 -0.595889 2.348736 0.000000 1 2.222947 -0.800514 0.000000 1 1.843180 1.558230 0.000000 And the relevant part of the log file that shows the error is and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009. ****************************************** Gaussian 09: EM64L-G09RevA.02 11-Jun-2009 21-Jun-2013 ****************************************** %chk=3Dpyrimidineisomer3+_1CISD.chk %mem=3D400mw %nproc=3D8 Will use up to 8 processors via shared memory. -------------------------------------- # CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg -------------------------------------- QPErr --- A syntax error was detected in the input line. # CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg ' Last state=3D"GCL" TCursr=3D 1046 LCursr=3D 2 Error termination via Lnk1e in /usr/local/g09/l1.exe at Fri Jun 21 14:10:38= 2013. If someone can see what I did wrong, please let me know. The Gaussian docu= mentation in the G09 users guide has an output example, but no input exampl= es. Thanks! Sam --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640D53Frinzlerrichmond_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi,

 

I submitted a CISD job using the syntax indicated fo= r CIS on page 214 of Gaussian’s understanding chemistry, but the job = crashed because of incorrect syntax.

 

My .com file was:

 

%chk=3Dpyrimidineisomer3+_1CISD.chk

%mem=3D400mw

%nproc=3D8

# CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg

 

pyrimidine cation init geom from pyrimidineisomer3&#= 43;_1.log optimized final CCSD geometry

 

1  2

7    -1.013004   -1.023688&= nbsp;   0.000000

7     1.257779   -0.45= 9984    0.000000

6     0.229443   -1.32= 9309    0.000000

6    -1.337639    0.29= 0345    0.000000

6    -0.341126    1.28= 5594    0.000000

6     0.986267   = 0.876632    0.000000

1    -2.405334    0.53= 9673    0.000000

1    -0.595889    2.34= 8736    0.000000

1     2.222947   -0.80= 0514    0.000000

1     1.843180   = 1.558230    0.000000

 

 

And the relevant part of the log file that shows the= error is

 

and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.=

 ******************************************

Gaussian 09:  EM64L-G09RevA.02 11-Jun-2009=

         &nb= sp;      21-Jun-2013

 ******************************************

%chk=3Dpyrimidineisomer3+_1CISD.chk

%mem=3D400mw

%nproc=3D8

Will use up to    8 processors via sh= ared memory.

--------------------------------------

# CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg

--------------------------------------

QPErr --- A syntax error was detected in the input l= ine.

# CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg

   '

Last state=3D"GCL"

TCursr=3D 1046 LCursr=3D    2

Error termination via Lnk1e in /usr/local/g09/l1.exe= at Fri Jun 21 14:10:38 2013.

 

If someone can see what I did wrong, please let me k= now.  The Gaussian documentation in the G09 users guide has an output = example, but no input examples.

 

Thanks!

Sam

--_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640D53Frinzlerrichmond_-- From owner-chemistry@ccl.net Tue Jun 25 14:54:00 2013 From: "Bradley Welch bwelch5(a)slu.edu" To: CCL Subject: CCL:G: G09: Proper syntax for CISD Message-Id: <-48853-130625145252-30056-7g0sJY/SmDgupaJ2xVOi2Q * server.ccl.net> X-Original-From: Bradley Welch Content-Type: multipart/alternative; boundary=f46d04428fd6c0654004dfff088e Date: Tue, 25 Jun 2013 13:52:43 -0500 MIME-Version: 1.0 Sent to CCL by: Bradley Welch [bwelch5_+_slu.edu] --f46d04428fd6c0654004dfff088e Content-Type: text/plain; charset=windows-1252 Content-Transfer-Encoding: quoted-printable Abrash, For the CIS excited state calculation you would put it as CIS(D,NStates=3D4= ) Hope this helps On Tue, Jun 25, 2013 at 12:43 PM, Abrash, Sam sabrash{:}richmond.edu < owner-chemistry%%ccl.net> wrote: > Hi,**** > > ** ** > > I submitted a CISD job using the syntax indicated for CIS on page 214 of > Gaussian=92s understanding chemistry, but the job crashed because of > incorrect syntax.**** > > ** ** > > My .com file was:**** > > ** ** > > %chk=3Dpyrimidineisomer3+_1CISD.chk**** > > %mem=3D400mw**** > > %nproc=3D8 **** > > # CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg**** > > ** ** > > pyrimidine cation init geom from pyrimidineisomer3+_1.log optimized final > CCSD geometry**** > > ** ** > > 1 2**** > > 7 -1.013004 -1.023688 0.000000**** > > 7 1.257779 -0.459984 0.000000**** > > 6 0.229443 -1.329309 0.000000**** > > 6 -1.337639 0.290345 0.000000**** > > 6 -0.341126 1.285594 0.000000**** > > 6 0.986267 0.876632 0.000000**** > > 1 -2.405334 0.539673 0.000000**** > > 1 -0.595889 2.348736 0.000000**** > > 1 2.222947 -0.800514 0.000000**** > > 1 1.843180 1.558230 0.000000**** > > ** ** > > ** ** > > And the relevant part of the log file that shows the error is**** > > ** ** > > and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.**** > > **** > > ********************************************** > > Gaussian 09: EM64L-G09RevA.02 11-Jun-2009**** > > 21-Jun-2013 **** > > ********************************************** > > %chk=3Dpyrimidineisomer3+_1CISD.chk**** > > %mem=3D400mw**** > > %nproc=3D8**** > > Will use up to 8 processors via shared memory.**** > > --------------------------------------**** > > # CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg**** > > --------------------------------------**** > > QPErr --- A syntax error was detected in the input line.**** > > # CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg**** > > '**** > > Last state=3D"GCL"**** > > TCursr=3D 1046 LCursr=3D 2**** > > Error termination via Lnk1e in /usr/local/g09/l1.exe at Fri Jun 21 > 14:10:38 2013.**** > > ** ** > > If someone can see what I did wrong, please let me know. The Gaussian > documentation in the G09 users guide has an output example, but no input > examples.**** > > ** ** > > Thanks!**** > > Sam**** > --=20 Bradley Welch Saint Louis University Monsanto Hall Room 218 --f46d04428fd6c0654004dfff088e Content-Type: text/html; charset=windows-1252 Content-Transfer-Encoding: quoted-printable
Abrash,=A0

For the CIS excited state ca= lculation you would put it as CIS(D,NStates=3D4)

H= ope this helps


On Tue, Jun 25, 2013 at 12:43 PM, Abrash, Sam sabrash{:}richmond.edu <owner-chemistry%%ccl.net> wrote:

Hi,

=A0

I submitted a CISD job using the syntax indicated fo= r CIS on page 214 of Gaussian=92s understanding chemistry, but the job cras= hed because of incorrect syntax.

=A0

My .com file was:

=A0

%chk=3Dpyrimidineisomer3+_1CISD.chk

%mem=3D400mw

%nproc=3D8

# CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg<= u>

=A0

pyrimidine cation init geom from pyrimidineisomer3+_= 1.log optimized final CCSD geometry

=A0

1=A0 2

7=A0=A0=A0 -1.013004=A0=A0 -1.023688=A0=A0=A0 0.0000= 00

7=A0=A0=A0=A0 1.257779=A0=A0 -0.459984=A0=A0=A0 0.00= 0000

6=A0=A0=A0=A0 0.229443=A0=A0 -1.329309=A0=A0=A0 0.00= 0000

6=A0=A0=A0 -1.337639=A0=A0=A0 0.290345=A0=A0=A0 0.00= 0000

6=A0=A0=A0 -0.341126=A0=A0=A0 1.285594=A0=A0=A0 0.00= 0000

6=A0=A0=A0=A0 0.986267=A0=A0=A0 0.876632=A0=A0=A0 0.= 000000

1=A0=A0=A0 -2.405334=A0=A0=A0 0.539673=A0=A0=A0 0.00= 0000

1=A0=A0=A0 -0.595889=A0=A0=A0 2.348736=A0=A0=A0 0.00= 0000

1=A0=A0=A0=A0 2.222947=A0=A0 -0.800514=A0=A0=A0 0.00= 0000

1=A0=A0=A0=A0 1.843180=A0=A0=A0 1.558230=A0=A0=A0 0.= 000000

=A0

=A0

And the relevant part of the log file that shows the= error is

=A0

and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.=

=A0******************************************=

Gaussian 09:=A0 EM64L-G09RevA.02 11-Jun-2009<= u>

=A0 =A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A0=A021-Jun= -2013

=A0******************************************=

%chk=3Dpyrimidineisomer3+_1CISD.chk

%mem=3D400mw

%nproc=3D8

Will use up to=A0=A0=A0 8 processors via shared memo= ry.

--------------------------------------=

# CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg<= u>

--------------------------------------=

QPErr --- A syntax error was detected in the input l= ine.

# CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg<= u>

=A0=A0 '

Last state=3D"GCL"

TCursr=3D 1046 LCursr=3D=A0=A0=A0 2

Error termination via Lnk1e in /usr/local/g09/l1.exe= at Fri Jun 21 14:10:38 2013.

=A0

If someone can see what I did wrong, please let me k= now.=A0 The Gaussian documentation in the G09 users guide has an output exa= mple, but no input examples.

=A0

Thanks!

Sam




--
Bradley Welc= h
Saint Louis University
Monsanto Hall Room 218
--f46d04428fd6c0654004dfff088e-- From owner-chemistry@ccl.net Tue Jun 25 15:50:00 2013 From: "Abrash, Sam sabrash=richmond.edu" To: CCL Subject: CCL:G: G09: Proper syntax for CISD Message-Id: <-48854-130625154858-5377-cbV0rbiQ1m7TA+HWI8aHlA]-[server.ccl.net> X-Original-From: "Abrash, Sam" Content-Language: en-US Content-Type: multipart/alternative; boundary="_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640DB09rinzlerrichmond_" Date: Tue, 25 Jun 2013 19:48:43 +0000 MIME-Version: 1.0 Sent to CCL by: "Abrash, Sam" [sabrash===richmond.edu] --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640DB09rinzlerrichmond_ Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi Everyone, The Gaussian help people cleared up the problem for me. Thanks! Sam > From: owner-chemistry+sabrash=3D=3Drichmond.edu.:.ccl.net [mailto:owner-chemi= stry+sabrash=3D=3Drichmond.edu.:.ccl.net] On Behalf Of Abrash, Sam sabrash{:}= richmond.edu Sent: Tuesday, June 25, 2013 1:43 PM To: Abrash, Sam Subject: CCL:G: G09: Proper syntax for CISD Hi, I submitted a CISD job using the syntax indicated for CIS on page 214 of Ga= ussian's understanding chemistry, but the job crashed because of incorrect = syntax. My .com file was: %chk=3Dpyrimidineisomer3+_1CISD.chk %mem=3D400mw %nproc=3D8 # CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg pyrimidine cation init geom from pyrimidineisomer3+_1.log optimized final C= CSD geometry 1 2 7 -1.013004 -1.023688 0.000000 7 1.257779 -0.459984 0.000000 6 0.229443 -1.329309 0.000000 6 -1.337639 0.290345 0.000000 6 -0.341126 1.285594 0.000000 6 0.986267 0.876632 0.000000 1 -2.405334 0.539673 0.000000 1 -0.595889 2.348736 0.000000 1 2.222947 -0.800514 0.000000 1 1.843180 1.558230 0.000000 And the relevant part of the log file that shows the error is and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009. ****************************************** Gaussian 09: EM64L-G09RevA.02 11-Jun-2009 21-Jun-2013 ****************************************** %chk=3Dpyrimidineisomer3+_1CISD.chk %mem=3D400mw %nproc=3D8 Will use up to 8 processors via shared memory. -------------------------------------- # CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg -------------------------------------- QPErr --- A syntax error was detected in the input line. # CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg ' Last state=3D"GCL" TCursr=3D 1046 LCursr=3D 2 Error termination via Lnk1e in /usr/local/g09/l1.exe at Fri Jun 21 14:10:38= 2013. If someone can see what I did wrong, please let me know. The Gaussian docu= mentation in the G09 users guide has an output example, but no input exampl= es. Thanks! Sam --_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640DB09rinzlerrichmond_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable

Hi Everyone,

 

The Gaussian help peop= le cleared up the problem for me.

 

Thanks!

Sam<= /p>

 

From: owner-ch= emistry+sabrash=3D=3Drichmond.edu.:.ccl.net [mailto:owner-chemistry+s= abrash=3D=3Drichmond.edu.:.ccl.net] On Behalf Of Abrash, Sam sabrash{:}richmond.edu
Sent: Tuesday, June 25, 2013 1:43 PM
To: Abrash, Sam
Subject: CCL:G: G09: Proper syntax for CISD

 

Hi,

 

I submitted a CISD job using the syntax indicated fo= r CIS on page 214 of Gaussian’s understanding chemistry, but the job = crashed because of incorrect syntax.

 

My .com file was:

 

%chk=3Dpyrimidineisomer3+_1CISD.chk

%mem=3D400mw

%nproc=3D8

# CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg

 

pyrimidine cation init geom from pyrimidineisomer3&#= 43;_1.log optimized final CCSD geometry

 

1  2

7    -1.013004   -1.023688&= nbsp;   0.000000

7     1.257779   -0.45= 9984    0.000000

6     0.229443   -1.32= 9309    0.000000

6    -1.337639    0.29= 0345    0.000000

6    -0.341126    1.28= 5594    0.000000

6     0.986267   = 0.876632    0.000000

1    -2.405334    0.53= 9673    0.000000

1    -0.595889    2.34= 8736    0.000000

1     2.222947   -0.80= 0514    0.000000

1     1.843180   = 1.558230    0.000000

 

 

And the relevant part of the log file that shows the= error is

 

and D. J. Fox, Gaussian, Inc., Wallingford CT, 2009.=

 

 ******************************************

Gaussian 09:  EM64L-G09RevA.02 11-Jun-2009=

         &nb= sp;      21-Jun-2013

 ******************************************

%chk=3Dpyrimidineisomer3+_1CISD.chk

%mem=3D400mw

%nproc=3D8

Will use up to    8 processors via sh= ared memory.

--------------------------------------

# CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg

--------------------------------------

QPErr --- A syntax error was detected in the input l= ine.

# CISD=3D(NStates=3D4)/aug-cc-pVTZ Pop=3DReg

   '

Last state=3D"GCL"

TCursr=3D 1046 LCursr=3D    2

Error termination via Lnk1e in /usr/local/g09/l1.exe= at Fri Jun 21 14:10:38 2013.

 

If someone can see what I did wrong, please let me k= now.  The Gaussian documentation in the G09 users guide has an output = example, but no input examples.

 

Thanks!

Sam

--_000_A7C78D2AEE62DB40B9CB1ADE9D5990A25640DB09rinzlerrichmond_-- From owner-chemistry@ccl.net Tue Jun 25 16:49:00 2013 From: "Daniel Casimir casimir.daniel%a%gmail.com" To: CCL Subject: CCL: AIREBO Potential in Tinker Message-Id: <-48855-130625155403-8945-j3OzxHNopRRcfLrNx3yGWA**server.ccl.net> X-Original-From: Daniel Casimir Content-Type: multipart/alternative; boundary=047d7b677798b4e9b204dfffe3c6 Date: Tue, 25 Jun 2013 15:53:56 -0400 MIME-Version: 1.0 Sent to CCL by: Daniel Casimir [casimir.daniel-x-gmail.com] --047d7b677798b4e9b204dfffe3c6 Content-Type: text/plain; charset=ISO-8859-1 Has anyone been able to implement the airebo potential from the LAMMPS MD simulation package into tinker? v/r, dc --047d7b677798b4e9b204dfffe3c6 Content-Type: text/html; charset=ISO-8859-1
Has anyone been able to implement the airebo potential from the LAMMPS MD simulation package into tinker?



v/r,

dc
--047d7b677798b4e9b204dfffe3c6--